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What you describe reads like a sensor issue more than mechanical issue(fuel flow)
All Engine computers have two operating modes
Open Loop, this is used when engine is cold, computer uses air/fuel mix tables in Memory and runs engine Rich(choked) with higher idle, not using most sensors
Closed Loop, O2 sensors need to be above 600degF to work, so engine needs to warm up a bit for these to "come on-line"
O2 sensors are the Feedback data the computer needs to adjust the air/fuel mix "on the fly"
So in Closed Loop computer is calculating air/fuel mix on its own, based on sensor INPUT and Feedback
It reads like your problem starts when computer switches over to Closed Loop, depending on outside temp this can take up to 10min of drive time
First on the list are the O2 sensors, 1994 4.0l will have two, one on each side of exhaust system
O2s only last 12 years or 100k miles, they simply run out of the chemical needed to detect oxygen in exhaust, no codes are set until they completely fail
O2s are the ONLY feedback the computer has there is no comparison available like with other sensors
So if they are older just change them, may or may not be the problem, but MPG will get better for sure if they are older
Clean the MAF sensor, easy to do and often the cause of "bucking" in the 4.0ls
MAF sensor "weighs" the incoming air
Gasoline needs an air/fuel mix of 14.7/1, and thats a WEIGHT ratio
14.7 pounds of air to 1 pound of gasoline
14.7grams of air to 1 gram of gasoline
Gasoline tends to weight the same cold or warm
Air on the other hand gets lighter warm and heavier when cold, i.e. "hot air rises" because its lighter
If MAF sensor is dirty then computer in Closed Loop is basing the air/fuel mix on the wrong data
If you had an injector issue or low fuel pressure it would effect engine operation cold or warm
So the "runs OK cold, but stumbles when warm" would indicate its not mechanical issue, like fuel flow